In the manual for MACS2, there is the following statement in the information about the --shift option: "Note, you can't set values other than 0 if format is BAMPE or BEDPE for paired-end data. Default is 0"
Is this also the case if the format is set as BAM or can I have different shift sizes with BAM? The command I would like to use to analyse my ATAC-seq data is as follows:
macs2 callpeak <input file> -f BAM --no-model --shift -100 --extsize 200 --keep-dup-all --call-summits
Many thanks, Lucy